Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes

Li, Jingyi Jessica; Chew, Guo-Liang; Biggin, Mark Douglas

doi:10.1186/s13059-019-1761-9

Title: Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes

Journal Article · 09 August 2019 · Genome Biology (Online)

DOI: https://doi.org/10.1186/s13059-019-1761-9 · OSTI ID:1626948

Li, Jingyi Jessica ^[1]; Chew, Guo-Liang ^[2];

^[3]

University of California, Los Angeles, CA (United States). Department of Statistics, Department of Biomathematics, and Department of Human Genetics
Fred Hutchinson Cancer Research Center, Seattle, WA (United States). Computational Biology Program, Public Health Sciences and Basic Sciences Division
Lawrence Berkeley National Laboratory, Berkeley, CA (United States). Biological Systems and Engineering Division

General translational cis-elements are present in the mRNAs of all genes and affect the recruitment, assembly, and progress of preinitiation complexes and the ribosome under many physiological states. These elements include mRNA folding, upstream open reading frames, specific nucleotides flanking the initiating AUG codon, protein coding sequence length, and codon usage. The quantitative contributions of these sequence features and how and why they coordinate to control translation rates are not well understood.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626948

Journal Information:: Genome Biology (Online), Vol. 20, Issue 1; ISSN 1474-760X

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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G-quadruplex located in the 5′UTR of the BAG-1 mRNA affects both its cap-dependent and cap-independent translation through global secondary structure maintenance Jodoin, Rachel; Carrier, Julie C.; Rivard, Nathalie Nucleic Acids Research, Vol. 47, Issue 19 https://doi.org/10.1093/nar/gkz777	journal	September 2019
G-quadruplex located in the 5′UTR of the BAG-1 mRNA affects both its cap-dependent and cap-independent translation through global secondary structure maintenance Jodoin, Rachel; Carrier, Julie C.; Rivard, Nathalie Nucleic Acids Research, Vol. 47, Issue 19 https://doi.org/10.1093/nar/gkz777	journal	September 2019
Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom Wallace, Edward W. J.; Maufrais, Corinne; Sales-Lee, Jade Nucleic Acids Research, Vol. 48, Issue 5 https://doi.org/10.1093/nar/gkaa060	journal	February 2020
Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom Wallace, Edward W. J.; Maufrais, Corinne; Sales-Lee, Jade Nucleic Acids Research, Vol. 48, Issue 5 https://doi.org/10.1093/nar/gkaa060	journal	February 2020

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Additional file 1: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461618 The current record is supplemented by this text	text	January 2019
Additional file 11: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461612 The current record is supplemented by this text	text	January 2019
Additional file 3: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461633.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 2: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461624 The current record is supplemented by this dataset	dataset	January 2019
Additional file 1: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461618.v1 The current record is supplemented by this text	text	January 2019
Additional file 4: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461642.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 3: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461633 The current record is supplemented by this dataset	dataset	January 2019
Additional file 4: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461642 The current record is supplemented by this dataset	dataset	January 2019
Additional file 2: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461624.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 5: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461648 The current record is supplemented by this dataset	dataset	January 2019
Additional file 8: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461669.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 9: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461675.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 7: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461663 The current record is supplemented by this dataset	dataset	January 2019
Additional file 6: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461657 The current record is supplemented by this dataset	dataset	January 2019
Additional file 10: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461603.v1 The current record is supplemented by this dataset	dataset	January 2019
Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.c.4613930 The current record is supplemented by this collection	collection	January 2019
Additional file 9: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461675 The current record is supplemented by this dataset	dataset	January 2019
Additional file 8: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461669 The current record is supplemented by this dataset	dataset	January 2019
Additional file 7: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461663.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 6: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461657.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 10: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461603 The current record is supplemented by this dataset	dataset	January 2019
Additional file 11: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461612.v1 The current record is supplemented by this text	text	January 2019
Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.c.4613930.v1 The current record is supplemented by this collection	collection	January 2019
Additional file 5: of Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes Li, Jingyi; Chew, Guo-Liang; Biggin, Mark https://doi.org/10.6084/m9.figshare.9461648.v1 The current record is supplemented by this dataset	dataset	January 2019